Searching journal content for articles similar to Pirola et al. 21 (10): 1601.

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  1. Research: A genome-wide survey reveals a diverse array of enhancers coordinates the Drosophila innate immune response
    • Lianne B Cohen,
    • Tamara Hadzic,
    • Caitlin Sauer,
    • Julia R Gibbs,
    • and Zeba Wunderlich
    Genome Res. April 15, 2026 gr.281432.125; Published in Advance April 15, 2026, doi:10.1101/gr.281432.125
    ...of how animals fight 32 infections. 33 Key words 34 Drosophila immunity/Immune-responsive enhancer/STARR-seq 35 36 Running Title 37 Genome-wide survey of fly immune enhancers 38 39 Introduction 40 When encountering pathogenic microbes, animals must regulate an effective immune response 41 to survive...
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  2. Mini-Review: Evolution of genome-wide methylation profiling technologies
    • Carolina Montano and
    • Winston Timp
    Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
    ...with paternal expression of IGF2 while the maternal copy is silenced (Monk et al. 2019). This is often regulated by epigenetic marks, including DNAm and histone posttranslational modifications. In the loss of imprinting disorders, either the active allele is silenced or the normally silent allele is abnormally...
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  3. Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
    • Kevin Moyung,
    • Yulong Li,
    • Heather K. MacAlpine,
    • Alexander J. Hartemink,
    • and David M. MacAlpine
    Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
    ...these universal instructions into cell type–specific programs that are able to respond to developmental and environmental cues. In part, this regulation is mediated by epigenetic mechanisms, which alter the accessibility of the chromatin in conjunction with changes in transcription factor (TF) and nucleosome...
  4. Research: Epigenetic characterization of pseudogenes across human tissues
    • Yunzhe Jiang,
    • Beatrice Borsari,
    • and Mark Gerstein
    Genome Res. April 15, 2026 gr.280768.125; Published in Advance April 15, 2026, doi:10.1101/gr.280768.125
    ..., relative to other noncoding genomic elements, their promoter architecture and epigenetic regulation remain incompletely understood. Here, we systematically characterize pseudogene promoters and compare them with those of protein-coding genes and long noncoding RNAs. To do this, we integrate matched...
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  5. Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
    • Marian F. Laughery,
    • Bastian Stark,
    • Benjamin Morledge-Hampton,
    • Steven A. Roberts,
    • and John J. Wyrick
    Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
    ...-in orientations in vitro (Song et al. 2011, 2014). However, to what extent nucleosomes modulate CPD deamination in other sequence contexts and across the of intact cells remains unclear.Genome-wide sequencing methods have emerged as powerful tools to understand how different genomic and chromatin contexts impact...
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  6. Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
    • Xuejing Wang and
    • Gerald Heckel
    Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
    ...window Figure 2. Genome-wide diversity and differentiation for common voles, M. arvalis, from the Orkney archipelago (brown) versus continental individuals (green). Density distributions (top) and Manhattan plots (bottom) for π, Tajima's D, and FST in 50 kb windows along the . Different chromosomes...
  7. Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
    • Samuel H. Kim,
    • Georgi K. Marinov,
    • and William J. Greenleaf
    Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
    ...abundances of accessible ssDNA and accessible DNA). (C) KAS-seq, ATAC-seq, and KAS-ATAC mitochondrial profiles in human GM12878 cells. (D) Fragment length distribution in biotin-ATAC-seq and KAS-ATAC libraries (GM12878 cells). (E) Genome-wide TSS metaprofiles for biotin-ATAC-seq and KAS-ATAC libraries (GM...
  8. Method: Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End
    • Lucinda C. Xiao,
    • Ayush Semwal,
    • Brianna St John,
    • Kathleen Zeglinski,
    • Shian Su,
    • James Lancaster,
    • Shifeng Xue,
    • Bruno Reversade,
    • Matthew E. Ritchie,
    • Frédérique Magdinier,
    • Marnie E. Blewitt,
    • and Quentin Gouil
    Genome Res. April 2026 36: 827-848; Published in Advance March 23, 2026, doi:10.1101/gr.280907.125
    ...the need for methods that can more comprehensively characterize the genetics and epigenetics of D4Z4 regulation.Until recently, study of D4Z4 has been limited by the low resolution and/or low read length of prior techniques. Southern blotting has long been the “gold standard” for FSHD molecular testing...
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  9. Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
    • Shudi Zhao,
    • Yuedong Li,
    • Guanping Chen,
    • Xingyang Wang,
    • Nan Chen,
    • and Xiaofeng Wu
    Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
    ...silencing (Tserel et al. 2010; Padeken et al. 2022).To testify the roles of these epigenomic signatures in regulating the transcriptional activity, ATAC-seq and H3K27ac ChIP-seq data obtained in our previous study, together with ChIP-seq data of several other histone modifications obtained from public...
  10. Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
    • Xiu Fan,
    • Qili Qian,
    • Wenran Li,
    • Tianzi Liu,
    • Changqing Zeng,
    • Peilin Jia,
    • Huandong Lin,
    • Xin Gao,
    • Li Jin,
    • Mingfeng Xia,
    • Sijia Wang,
    • and Fan Liu
    Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
    ..., distinguishing it from the linear age-associated methylation changes at epigenetic clock sites (Fraga et al. 2005; Horvath and Raj 2018; Seale et al. 2022). Importantly, epigenetic drift likely unfolds more gradually across wider temporal windows, capturing interindividual and cellular heterogeneity in a way...
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